After samples have been added and associated with valid data files, a data node will appear in the Analyses tab (Figure 201). The Analyses tab is where different analysis tools and the corresponding reports are accessed.

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The Analyses tab contains two elements: data nodes (circles) and task nodes (rounded rectangles) connected by lines and arrows. Collectively, they represent a data analysis pipeline. 
Data nodes (Figure 212) may represent a file imported into the project, or a file generated by Partek Flow as an output of a task (e.g., alignment of FASTQ files generates BAM files).

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Task nodes (Figure 223) represent the analysis steps performed on the data within a project. For details on the tasks available in Partek Flow, see the specific chapters of this user manual dedicated to the different tasks.

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Only the tasks that are available for the selected data node will be listed in the menu. For data nodes, actions that can be performed on that specific data type will appear.

In Figure 234, a node that contains Unaligned reads is selected (bold black line). The tasks listed are the ones that can be performed on unaligned data (QA/QC, Pre-analysis tools, and Aligners).

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After a task is performed on a data node, a new task node is created and connected to the original data node. Depending on the task, a new data node may automatically be generated that contains the resulting data.

In Figure 245, alignment was performed on the unaligned reads. Two additional nodes were added: a task node for Align reads and an output data node containing the Aligned reads.

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To run a task, select a data node and then locate the task you wish to perform from the task pane. Mouse over to see a description of the action to be performed. Click the specific task, set the additional parameters (Figure 256), and click Finish. The task will be scheduled, the display will refresh, and the screen will return to the project's Analyses tab.

In Figure 256, the STAR aligner was selected and the choices for the aligner index and additional alignment options appeared.

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Tasks that are currently running (or scheduled in the queue) appear as translucent nodes. The progress of the task is indicated by the progress bar within the task node. Hovering the mouse pointer over the node will highlight the related nodes (with a thin black outline) and display the status of the task (Figure 267).

If a task is expected to generate data nodes, expected nodes appear even before the task is completed. They will have a lighter shade of color to indicate that they have not yet been generated as the task is still being performed. Once all tasks are done, all nodes would appear in the same shade.

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Tasks can only be cancelled or deleted by the user that started the task. Running or pending tasks can be canceled by clicking the right mouse button on the task node and then selecting Cancel (Figure 278). Alternatively, the task node may be selected and the Cancel task selected from the task pane.

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Cancelled or failed tasks are flagged by small red circles with exclamation points on the tasks nodes. Data nodes connected to incomplete tasks are also incomplete as no output can be generated (Figure 289). For failure due to errors, see the Task details.

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To delete tasks from the project click the right mouse button on the task node and then select Delete (Figure 2910). Alternatively, click the task node and select Delete task from the task pane. The nodes downstream of this task will be deleted. However, deleting the output files is optional (Figure 289, inset).

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Selecting a task node will reveal a menu pane with two sections: Task results and Task actions (Figure 3011).

Items from the Task results section inform on the action performed in that node. Certain tasks generate a Task report (Figure 3112), which include any tables or charts that the task may have produced.

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The Task details shows detailed diagnostic information about the task (Figure 3213). It includes the duration and parameters of the task, lists of input and output files, and the actual commands (in the command line) that were run.

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Another action available for a task node is Add task description (Figure 3314), which is a way to add notes to the project. The user can enter a description, which will be displayed when the mouse pointer is hovered over the task node.

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